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Cadavid JL, Li NT, McGuigan AP. Bridging systems biology and tissue engineering: Unleashing the full potential of complex 3D in vitro tissue models of disease. BIOPHYSICS REVIEWS 2024; 5:021301. [PMID: 38617201 PMCID: PMC11008916 DOI: 10.1063/5.0179125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/12/2024] [Indexed: 04/16/2024]
Abstract
Rapid advances in tissue engineering have resulted in more complex and physiologically relevant 3D in vitro tissue models with applications in fundamental biology and therapeutic development. However, the complexity provided by these models is often not leveraged fully due to the reductionist methods used to analyze them. Computational and mathematical models developed in the field of systems biology can address this issue. Yet, traditional systems biology has been mostly applied to simpler in vitro models with little physiological relevance and limited cellular complexity. Therefore, integrating these two inherently interdisciplinary fields can result in new insights and move both disciplines forward. In this review, we provide a systematic overview of how systems biology has been integrated with 3D in vitro tissue models and discuss key application areas where the synergies between both fields have led to important advances with potential translational impact. We then outline key directions for future research and discuss a framework for further integration between fields.
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2
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Mostofinejad A, Romero DA, Brinson D, Marin-Araujo AE, Bazylak A, Waddell TK, Haykal S, Karoubi G, Amon CH. In silico model development and optimization of in vitro lung cell population growth. PLoS One 2024; 19:e0300902. [PMID: 38748626 PMCID: PMC11095723 DOI: 10.1371/journal.pone.0300902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/04/2024] [Indexed: 05/19/2024] Open
Abstract
Tissue engineering predominantly relies on trial and error in vitro and ex vivo experiments to develop protocols and bioreactors to generate functional tissues. As an alternative, in silico methods have the potential to significantly reduce the timelines and costs of experimental programs for tissue engineering. In this paper, we propose a methodology to formulate, select, calibrate, and test mathematical models to predict cell population growth as a function of the biochemical environment and to design optimal experimental protocols for model inference of in silico model parameters. We systematically combine methods from the experimental design, mathematical statistics, and optimization literature to develop unique and explainable mathematical models for cell population dynamics. The proposed methodology is applied to the development of this first published model for a population of the airway-relevant bronchio-alveolar epithelial (BEAS-2B) cell line as a function of the concentration of metabolic-related biochemical substrates. The resulting model is a system of ordinary differential equations that predict the temporal dynamics of BEAS-2B cell populations as a function of the initial seeded cell population and the glucose, oxygen, and lactate concentrations in the growth media, using seven parameters rigorously inferred from optimally designed in vitro experiments.
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Affiliation(s)
- Amirmahdi Mostofinejad
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - David A. Romero
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Dana Brinson
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alba E. Marin-Araujo
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Latner Research Laboratories, Division of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Aimy Bazylak
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Thomas K. Waddell
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Latner Research Laboratories, Division of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Siba Haykal
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Division of Plastic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Golnaz Karoubi
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Latner Research Laboratories, Division of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Cristina H. Amon
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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3
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Ashmore-Harris C, Antonopoulou E, Finney SM, Vieira MR, Hennessy MG, Muench A, Lu WY, Gadd VL, El Haj AJ, Forbes SJ, Waters SL. Exploiting in silico modelling to enhance translation of liver cell therapies from bench to bedside. NPJ Regen Med 2024; 9:19. [PMID: 38724586 PMCID: PMC11081951 DOI: 10.1038/s41536-024-00361-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Cell therapies are emerging as promising treatments for a range of liver diseases but translational bottlenecks still remain including: securing and assessing the safe and effective delivery of cells to the disease site; ensuring successful cell engraftment and function; and preventing immunogenic responses. Here we highlight three therapies, each utilising a different cell type, at different stages in their clinical translation journey: transplantation of multipotent mesenchymal stromal/signalling cells, hepatocytes and macrophages. To overcome bottlenecks impeding clinical progression, we advocate for wider use of mechanistic in silico modelling approaches. We discuss how in silico approaches, alongside complementary experimental approaches, can enhance our understanding of the mechanisms underlying successful cell delivery and engraftment. Furthermore, such combined theoretical-experimental approaches can be exploited to develop novel therapies, address safety and efficacy challenges, bridge the gap between in vitro and in vivo model systems, and compensate for the inherent differences between animal model systems and humans. We also highlight how in silico model development can result in fewer and more targeted in vivo experiments, thereby reducing preclinical costs and experimental animal numbers and potentially accelerating translation to the clinic. The development of biologically-accurate in silico models that capture the mechanisms underpinning the behaviour of these complex systems must be reinforced by quantitative methods to assess cell survival post-transplant, and we argue that non-invasive in vivo imaging strategies should be routinely integrated into transplant studies.
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Affiliation(s)
- Candice Ashmore-Harris
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | | | - Simon M Finney
- Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK
| | - Melissa R Vieira
- Healthcare Technologies Institute (HTI), Institute of Translational Medicine, University of Birmingham, Birmingham, B15 2TH, UK
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, B15 2TH, UK
| | - Matthew G Hennessy
- Department of Engineering Mathematics, University of Bristol, BS8 1TW, Bristol, UK
| | - Andreas Muench
- Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK
| | - Wei-Yu Lu
- Centre for Inflammation Research, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Victoria L Gadd
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Alicia J El Haj
- Healthcare Technologies Institute (HTI), Institute of Translational Medicine, University of Birmingham, Birmingham, B15 2TH, UK
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Birmingham, B15 2TH, UK
| | - Stuart J Forbes
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - Sarah L Waters
- Mathematical Institute, University of Oxford, Oxford, OX2 6GG, UK.
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4
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Durmaz A, Visconte V. Capturing the unpredictability of stem cells. eLife 2024; 13:e95513. [PMID: 38427029 PMCID: PMC10906994 DOI: 10.7554/elife.95513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A new mathematical model that can be applied to both single-cell and bulk DNA sequencing data sheds light on the processes governing population dynamics in stem cells.
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Affiliation(s)
- Arda Durmaz
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland ClinicClevelandUnited States
| | - Valeria Visconte
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland ClinicClevelandUnited States
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5
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Thangadurai M, Srinivasan SS, Sekar MP, Sethuraman S, Sundaramurthi D. Emerging perspectives on 3D printed bioreactors for clinical translation of engineered and bioprinted tissue constructs. J Mater Chem B 2024; 12:350-381. [PMID: 38084021 DOI: 10.1039/d3tb01847d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
3D printed/bioprinted tissue constructs are utilized for the regeneration of damaged tissues and as in vitro models. Most of the fabricated 3D constructs fail to undergo functional maturation in conventional in vitro settings. There is a challenge to provide a suitable niche for the fabricated tissue constructs to undergo functional maturation. Bioreactors have emerged as a promising tool to enhance tissue maturation of the engineered constructs by providing physical/biological cues along with a controlled nutrient supply under dynamic in vitro conditions. Bioreactors provide an ambient microenvironment most appropriate for the development of functionally matured tissue constructs by promoting cell proliferation, differentiation, and maturation for transplantation and drug screening applications. Due to the huge cost and limited availability of commercial bioreactors, there is a need to develop strategies to make customized bioreactors. Additive manufacturing (AM) may be a viable tool to fabricate custom designed bioreactors with better efficiency and at low cost. In this review, we have extensively discussed the importance of bioreactors in functionalizing tissue engineered/3D bioprinted scaffolds for bone, cartilage, skeletal muscle, nerve, and vascular tissue. In addition, the importance and fabrication of customized 3D printed bioreactors for the maturation of tissue engineered constructs are discussed in detail. Finally, the current challenges and future perspectives in translating commercial and custom 3D printed bioreactors for clinical applications are outlined.
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Affiliation(s)
- Madhumithra Thangadurai
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials, ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, India.
| | - Sai Sadhananth Srinivasan
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials, ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, India.
| | - Muthu Parkkavi Sekar
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials, ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, India.
| | - Swaminathan Sethuraman
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials, ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, India.
| | - Dhakshinamoorthy Sundaramurthi
- Tissue Engineering & Additive Manufacturing (TEAM) Lab, Centre for Nanotechnology & Advanced Biomaterials, ABCDE Innovation Centre, School of Chemical & Biotechnology, SASTRA Deemed University, India.
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6
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Hardman D, Hennig K, Gomes ER, Roman W, Bernabeu MO. An in vitro agent-based modelling approach to optimization of culture medium for generating muscle cells. J R Soc Interface 2024; 21:20230603. [PMID: 38228184 PMCID: PMC10791523 DOI: 10.1098/rsif.2023.0603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024] Open
Abstract
Methodologies for culturing muscle tissue are currently lacking in terms of quality and quantity of mature cells produced. We analyse images from in vitro experiments to quantify the effects of culture media composition on mouse-derived myoblast behaviour and myotube quality. Metrics of early indicators of cell quality were defined. Images of muscle cell differentiation reveal that altering culture media significantly affects quality indicators and myoblast migratory behaviours. To study the effects of early-stage cell behaviours on mature cell quality, metrics drawn from experimental images or inferred by approximate Bayesian computation (ABC) were applied as inputs to an agent-based model (ABM) of skeletal muscle cell differentiation with quality indicator metrics as outputs. Computational modelling was used to inform further in vitro experiments to predict the optimum media composition for culturing muscle cells. Our results suggest that myonuclei production in myotubes is inversely related to early-stage nuclei fusion index and that myonuclei density and spatial distribution are correlated with residence time of fusing myoblasts, the age at which myotube-myotube fusion ends and the repulsion force between myonuclei. Culture media with 5% serum was found to produce the optimum cell quality and to make muscle cells cultured in a neuron differentiation medium viable.
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Affiliation(s)
- David Hardman
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Katharina Hennig
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Edgar R. Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - William Roman
- Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Miguel O. Bernabeu
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh EH16 4UX, UK
- The Bayes Centre, University of Edinburgh, Edinburgh EH8 9BT, UK
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7
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Berg M, Eleftheriadou D, Phillips JB, Shipley RJ. Mathematical modelling with Bayesian inference to quantitatively characterize therapeutic cell behaviour in nerve tissue engineering. J R Soc Interface 2023; 20:20230258. [PMID: 37669694 PMCID: PMC10480012 DOI: 10.1098/rsif.2023.0258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/15/2023] [Indexed: 09/07/2023] Open
Abstract
Cellular engineered neural tissues have significant potential to improve peripheral nerve repair strategies. Traditional approaches depend on quantifying tissue behaviours using experiments in isolation, presenting a challenge for an overarching framework for tissue design. By comparison, mathematical cell-solute models benchmarked against experimental data enable computational experiments to be performed to test the role of biological/biophysical mechanisms, as well as to explore the impact of different design scenarios and thus accelerate the development of new treatment strategies. Such models generally consist of a set of continuous, coupled, partial differential equations relying on a number of parameters and functional forms. They necessitate dedicated in vitro experiments to be informed, which are seldom available and often involve small datasets with limited spatio-temporal resolution, generating uncertainties. We address this issue and propose a pipeline based on Bayesian inference enabling the derivation of experimentally informed cell-solute models describing therapeutic cell behaviour in nerve tissue engineering. We apply our pipeline to three relevant cell types and obtain models that can readily be used to simulate nerve repair scenarios and quantitatively compare therapeutic cells. Beyond parameter estimation, the proposed pipeline enables model selection as well as experiment utility quantification, aimed at improving both model formulation and experimental design.
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Affiliation(s)
- Maxime Berg
- Centre for Nerve Engineering, University College London, WC1E 6BT London, UK
- Department of Mechanical Engineering, University College London, WC1E 6BT London, UK
| | - Despoina Eleftheriadou
- Centre for Nerve Engineering, University College London, WC1E 6BT London, UK
- School of Pharmacy, University College London, WC1N 1AX London, UK
| | - James B. Phillips
- Centre for Nerve Engineering, University College London, WC1E 6BT London, UK
- School of Pharmacy, University College London, WC1N 1AX London, UK
| | - Rebecca J. Shipley
- Centre for Nerve Engineering, University College London, WC1E 6BT London, UK
- Department of Mechanical Engineering, University College London, WC1E 6BT London, UK
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8
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Fernández-Colino A, Kiessling F, Slabu I, De Laporte L, Akhyari P, Nagel SK, Stingl J, Reese S, Jockenhoevel S. Lifelike Transformative Materials for Biohybrid Implants: Inspired by Nature, Driven by Technology. Adv Healthc Mater 2023; 12:e2300991. [PMID: 37290055 DOI: 10.1002/adhm.202300991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/25/2023] [Indexed: 06/10/2023]
Abstract
Today's living world is enriched with a myriad of natural biological designs, shaped by billions of years of evolution. Unraveling the construction rules of living organisms offers the potential to create new materials and systems for biomedicine. From the close examination of living organisms, several concepts emerge: hierarchy, pattern repetition, adaptation, and irreducible complexity. All these aspects must be tackled to develop transformative materials with lifelike behavior. This perspective article highlights recent progress in the development of transformative biohybrid systems for applications in the fields of tissue regeneration and biomedicine. Advances in computational simulations and data-driven predictions are also discussed. These tools enable the virtual high-throughput screening of implant design and performance before committing to fabrication, thus reducing the development time and cost of biomimetic and biohybrid constructs. The ongoing progress of imaging methods also constitutes an essential part of this matter in order to validate the computation models and enable longitudinal monitoring. Finally, the current challenges of lifelike biohybrid materials, including reproducibility, ethical considerations, and translation, are discussed. Advances in the development of lifelike materials will open new biomedical horizons, where perhaps what is currently envisioned as science fiction will become a science-driven reality in the future.
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Affiliation(s)
- Alicia Fernández-Colino
- Department of Biohybrid & Medical Textiles (BioTex), AME-Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Forckenbeckstraße 55, 52074, Aachen, Germany
| | - Fabian Kiessling
- Institute for Experimental Molecular Imaging, Faculty of Medicine, RWTH Aachen University, Forckenbeckstraße 55, 52074, Aachen, Germany
| | - Ioana Slabu
- Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Laura De Laporte
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry (ITMC), RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- Advanced Materials for Biomedicine (AMB), Institute of Applied Medical Engineering (AME), University Hospital RWTH Aachen, Center for Biohybrid Medical Systems (CMBS), Forckenbeckstraße 55, 52074, Aachen, Germany
| | - Payam Akhyari
- Clinic for Cardiac Surgery, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Saskia K Nagel
- Applied Ethics Group, RWTH Aachen University, Theaterplatz 14, 52062, Aachen, Germany
| | - Julia Stingl
- Institute of Clinical Pharmacology, University Hospital RWTH Aachen, Wendlingweg 2, 52074, Aachen, Germany
| | - Stefanie Reese
- Institute of Applied Mechanics, RWTH Aachen University, Mies-van-der-Rohe-Str. 1, 52074, Aachen, Germany
| | - Stefan Jockenhoevel
- Department of Biohybrid & Medical Textiles (BioTex), AME-Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Forckenbeckstraße 55, 52074, Aachen, Germany
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9
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Montes-Olivas S, Legge D, Lund A, Fletcher AG, Williams AC, Marucci L, Homer M. In-silico and in-vitro morphometric analysis of intestinal organoids. PLoS Comput Biol 2023; 19:e1011386. [PMID: 37578984 PMCID: PMC10473498 DOI: 10.1371/journal.pcbi.1011386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/01/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023] Open
Abstract
Organoids offer a powerful model to study cellular self-organisation, the growth of specific tissue morphologies in-vitro, and to assess potential medical therapies. However, the intrinsic mechanisms of these systems are not entirely understood yet, which can result in variability of organoids due to differences in culture conditions and basement membrane extracts used. Improving the standardisation of organoid cultures is essential for their implementation in clinical protocols. Developing tools to assess and predict the behaviour of these systems may produce a more robust and standardised biological model to perform accurate clinical studies. Here, we developed an algorithm to automate crypt-like structure counting on intestinal organoids in both in-vitro and in-silico images. In addition, we modified an existing two-dimensional agent-based mathematical model of intestinal organoids to better describe the system physiology, and evaluated its ability to replicate budding structures compared to new experimental data we generated. The crypt-counting algorithm proved useful in approximating the average number of budding structures found in our in-vitro intestinal organoid culture images on days 3 and 7 after seeding. Our changes to the in-silico model maintain the potential to produce simulations that replicate the number of budding structures found on days 5 and 7 of in-vitro data. The present study aims to aid in quantifying key morphological structures and provide a method to compare both in-vitro and in-silico experiments. Our results could be extended later to 3D in-silico models.
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Affiliation(s)
- Sandra Montes-Olivas
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Danny Legge
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Abbie Lund
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
| | - Alexander G. Fletcher
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Ann C. Williams
- Colorectal Tumour Biology Group, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- BrisSynBio, Bristol, United Kingdom
| | - Martin Homer
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom
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10
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Laranjeira S, Roberton VH, Phillips JB, Shipley RJ. Perspectives on optimizing local delivery of drugs to peripheral nerves using mathematical models. WIREs Mech Dis 2023; 15:e1593. [PMID: 36624330 PMCID: PMC10909486 DOI: 10.1002/wsbm.1593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Drug therapies for treating peripheral nerve injury repair have shown significant promise in preclinical studies. Despite this, drug treatments are not used routinely clinically to treat patients with peripheral nerve injuries. Drugs delivered systemically are often associated with adverse effects to other tissues and organs; it remains challenging to predict the effective concentration needed at an injured nerve and the appropriate delivery strategy. Local drug delivery approaches are being developed to mitigate this, for example via injections or biomaterial-mediated release. We propose the integration of mathematical modeling into the development of local drug delivery protocols for peripheral nerve injury repair. Mathematical models have the potential to inform understanding of the different transport mechanisms at play, as well as quantitative predictions around the efficacy of individual local delivery protocols. We discuss existing approaches in the literature, including drawing from other research fields, and present a process for taking forward an integrated mathematical-experimental approach to accelerate local drug delivery approaches for peripheral nerve injury repair. This article is categorized under: Neurological Diseases > Molecular and Cellular Physiology Neurological Diseases > Computational Models Neurological Diseases > Biomedical Engineering.
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Affiliation(s)
- Simao Laranjeira
- UCL Mechanical EngineeringUCL Centre for Nerve EngineeringLondonLondonUK
| | | | - James B. Phillips
- UCL School of PharmacyUCL Centre for Nerve EngineeringLondonLondonUK
| | - Rebecca J. Shipley
- UCL Mechanical EngineeringUCL Centre for Nerve EngineeringLondonLondonUK
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11
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Implementing systems thinking and data science in the training of the regenerative medicine workforce. NPJ Regen Med 2022; 7:76. [PMID: 36566283 PMCID: PMC9790008 DOI: 10.1038/s41536-022-00271-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/05/2022] [Indexed: 12/25/2022] Open
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12
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Baranovskii DS, Klabukov ID, Arguchinskaya NV, Yakimova AO, Kisel AA, Yatsenko EM, Ivanov SA, Shegay PV, Kaprin AD. Adverse events, side effects and complications in mesenchymal stromal cell-based therapies. Stem Cell Investig 2022; 9:7. [PMID: 36393919 PMCID: PMC9659480 DOI: 10.21037/sci-2022-025] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/28/2022] [Indexed: 07/22/2023]
Abstract
Numerous clinical studies have shown a wide clinical potential of mesenchymal stromal cells (MSCs) application. However, recent experience has accumulated numerous reports of adverse events and side effects associated with MSCs therapy. Furthermore, the strategies and methods of MSCs therapy did not change significantly in recent decades despite the clinical impact and awareness of potential complications. An extended understanding of limitations could lead to a wider clinical implementation of safe cell therapies and avoid harmful approaches. Therefore, our objective was to summarize the possible negative effects observed during MSCs-based therapies. We were also aimed to discuss the risks caused by weaknesses in cell processing, including isolation, culturing, and storage. Cell processing and cell culture could dramatically influence cell population profile, change protein expression and cell differentiation paving the way for future negative effects. Long-term cell culture led to accumulation of chromosomal abnormalities. Overdosed antibiotics in culture media enhanced the risk of mycoplasma contamination. Clinical trials reported thromboembolism and fibrosis as the most common adverse events of MSCs therapy. Their delayed manifestation generally depends on the patient's individual phenotype and requires specific awareness during the clinical trials with obligatory inclusion in the patient' informed consents. Finally we prepared the safety checklist, recommended for clinical specialists before administration or planning of MSCs therapy.
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Affiliation(s)
- Denis S. Baranovskii
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ilya D. Klabukov
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
- Obninsk Institute for Nuclear Power Engineering of the National Research Nuclear University MEPhI, Obninsk, Russia
| | - Nadezhda V. Arguchinskaya
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Anna O. Yakimova
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Anastas A. Kisel
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Elena M. Yatsenko
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Sergei A. Ivanov
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Peter V. Shegay
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Andrey D. Kaprin
- National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
- Peoples’ Friendship University of Russia (RUDN University), Moscow, Russia
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13
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Kolasa M, Czerczak K, Fraczyk J, Szymanski L, Lewicki S, Bednarowicz A, Tarzynska N, Sikorski D, Szparaga G, Draczynski Z, Cierniak S, Brzoskowska U, Galita G, Majsterek I, Bociaga D, Krol P, Kolesinska B. Evaluation of Polysaccharide-Peptide Conjugates Containing the RGD Motif for Potential Use in Muscle Tissue Regeneration. MATERIALS (BASEL, SWITZERLAND) 2022; 15:6432. [PMID: 36143745 PMCID: PMC9503514 DOI: 10.3390/ma15186432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
New scaffold materials composed of biodegradable components are of great interest in regenerative medicine. These materials should be: stable, nontoxic, and biodegrade slowly and steadily, allowing the stable release of biodegradable and biologically active substances. We analyzed peptide-polysaccharide conjugates derived from peptides containing RGD motif (H-RGDS-OH (1), H-GRGDS-NH2 (2), and cyclo(RGDfC) (3)) and polysaccharides as scaffolds to select the most appropriate biomaterials for application in regenerative medicine. Based on the results of MTT and Ki-67 assays, we can state that the conjugates containing calcium alginate and the ternary nonwoven material were the most supportive of muscle tissue regeneration. Scanning electron microscopy imaging and light microscopy studies with hematoxylin-eosin staining showed that C2C12 cells were able to interact with the tested peptide-polysaccharide conjugates. The release factor (Q) varied depending on both the peptide and the structure of the polysaccharide matrix. LDH, Alamarblue®, Ki-67, and cell cycle assays indicated that peptides 1 and 2 were characterized by the best biological properties. Conjugates containing chitosan and the ternary polysaccharide nonwoven with peptide 1 exhibited very high antibacterial activity against Staphylococcus aureus and Klebsiella pneumoniae. Overall, the results of the study suggested that polysaccharide conjugates with peptides 1 and 2 can be potentially used in regenerative medicine.
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Affiliation(s)
- Marcin Kolasa
- Military Institute of Hygiene and Epidemiology, Department of Pharmacology and Toxicology, Kozielska 4, 01-163 Warsaw, Poland
| | - Katarzyna Czerczak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Lukasz Szymanski
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Science, Postępu 36A, 05-552 Magdalenka, Poland
| | - Slawomir Lewicki
- Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Science, Postępu 36A, 05-552 Magdalenka, Poland
| | - Anna Bednarowicz
- Institute of Material Sciences of Textiles and Polymer Composites, Faculty of Material Technologies and Textile Design, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Nina Tarzynska
- Institute of Material Sciences of Textiles and Polymer Composites, Faculty of Material Technologies and Textile Design, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Dominik Sikorski
- Institute of Material Sciences of Textiles and Polymer Composites, Faculty of Material Technologies and Textile Design, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Grzegorz Szparaga
- Institute of Material Sciences of Textiles and Polymer Composites, Faculty of Material Technologies and Textile Design, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Zbigniew Draczynski
- Institute of Material Sciences of Textiles and Polymer Composites, Faculty of Material Technologies and Textile Design, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | | | | | - Grzegorz Galita
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland
| | - Dorota Bociaga
- Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-537 Lodz, Poland
| | - Paulina Krol
- Lukasiewicz Research Network-Textile Research Institute, Brzezinska 5/15, 92-103 Lodz, Poland
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
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14
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Wu D, Zhao L, Sui B, Tan L, Lu L, Mao X, Liao G, Shi S, Cao Y, Yang X, Kou X. An Appearance Data-Driven Model Visualizes Cell State and Predicts Mesenchymal Stem Cell Regenerative Capacity. SMALL METHODS 2022; 6:e2200087. [PMID: 35674483 DOI: 10.1002/smtd.202200087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Mesenchymal stem cells (MSCs) are widely used in treating various diseases. However, lack of a reliable evaluation approach to characterize the potency of MSCs has dampened their clinical applications. Here, a function-oriented mathematical model is established to evaluate and predict the regenerative capacity (RC) of MSCs. Processed by exhaustive testing, the model excavates four optimal fitted indices, including nucleus roundness, nucleus/cytoplasm ratio, side-scatter height, and ERK1/2 from the given index combinations. Notably, three of them except ERK1/2 are cell appearance-associated features. The predictive power of the model is validated via screening experiments of these indices by predicting the RC of newly enrolled and chemical inhibitor-treated MSCs. Further RNA-sequencing analysis reveals that cell appearance-based indices may serve as major indicators to visualize the results of integration-weighted signals in and out of cells and reflect MSC stemness. In general, this study proposes an appearance data-driven predictive model for the RC and stemness of MSCs.
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Affiliation(s)
- Di Wu
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Oral and Maxillofacial Surgery, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Orthodontics, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Lu Zhao
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Bingdong Sui
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- State Key Laboratory of Military Stomatology, National Clinical Research Center for Oral Diseases, Shaanxi International Joint Research Center for Oral Diseases, Center for Tissue Engineering, School of Stomatology, The Fourth Military Medical University, Xi'an, 710032, China
| | - Lingping Tan
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Lu Lu
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xueli Mao
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Guiqing Liao
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Oral and Maxillofacial Surgery, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Songtao Shi
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Key Laboratory of Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yang Cao
- Hospital of Stomatology, Guanghua School of Stomatology, Department of Orthodontics, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
| | - Xiaobao Yang
- School of Physics and Optoelectronics, South China University of Technology, Guangzhou, 510640, China
| | - Xiaoxing Kou
- Hospital of Stomatology, Guanghua School of Stomatology, South China Center of Craniofacial Stem Cell Research, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, 510055, China
- Key Laboratory of Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
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15
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Allenby MC, Woodruff MA. Image analyses for engineering advanced tissue biomanufacturing processes. Biomaterials 2022; 284:121514. [DOI: 10.1016/j.biomaterials.2022.121514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
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16
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Maric DM, Velikic G, Maric DL, Supic G, Vojvodic D, Petric V, Abazovic D. Stem Cell Homing in Intrathecal Applications and Inspirations for Improvement Paths. Int J Mol Sci 2022; 23:ijms23084290. [PMID: 35457107 PMCID: PMC9027729 DOI: 10.3390/ijms23084290] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/26/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023] Open
Abstract
A transplanted stem cell homing is a directed migration from the application site to the targeted tissue. Intrathecal application of stem cells is their direct delivery to cerebrospinal fluid, which defines the homing path from the point of injection to the brain. In the case of neurodegenerative diseases, this application method has the advantage of no blood–brain barrier restriction. However, the homing efficiency still needs improvement and homing mechanisms elucidation. Analysis of current research results on homing mechanisms in the light of intrathecal administration revealed a discrepancy between in vivo and in vitro results and a gap between preclinical and clinical research. Combining the existing research with novel insights from cutting-edge biochips, nano, and other technologies and computational models may bridge this gap faster.
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Affiliation(s)
- Dusan M. Maric
- Department for Research and Development, Clinic Orto MD-Parks Dr Dragi Hospital, 21000 Novi Sad, Serbia;
- Faculty of Dentistry Pancevo, University Business Academy, 26000 Pancevo, Serbia
- Vincula Biotech Group, 11000 Belgrade, Serbia;
| | - Gordana Velikic
- Department for Research and Development, Clinic Orto MD-Parks Dr Dragi Hospital, 21000 Novi Sad, Serbia;
- Vincula Biotech Group, 11000 Belgrade, Serbia;
- Correspondence: (G.V.); (D.L.M.)
| | - Dusica L. Maric
- Department of Anatomy, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
- Correspondence: (G.V.); (D.L.M.)
| | - Gordana Supic
- Institute for Medical Research, Military Medical Academy, 11000 Belgrade, Serbia; (G.S.); (D.V.)
- Medical Faculty of Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
| | - Danilo Vojvodic
- Institute for Medical Research, Military Medical Academy, 11000 Belgrade, Serbia; (G.S.); (D.V.)
- Medical Faculty of Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
| | - Vedrana Petric
- Infectious Diseases Clinic, Clinical Center of Vojvodina, 21000 Novi Sad, Serbia;
- Department of Infectious Diseases, Faculty of Medicine, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Dzihan Abazovic
- Vincula Biotech Group, 11000 Belgrade, Serbia;
- Department for Regenerative Medicine, Biocell Hospital, 11000 Belgrade, Serbia
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17
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Iberite F, Gruppioni E, Ricotti L. Skeletal muscle differentiation of human iPSCs meets bioengineering strategies: perspectives and challenges. NPJ Regen Med 2022; 7:23. [PMID: 35393412 PMCID: PMC8991236 DOI: 10.1038/s41536-022-00216-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 03/01/2022] [Indexed: 12/31/2022] Open
Abstract
Although skeletal muscle repairs itself following small injuries, genetic diseases or severe damages may hamper its ability to do so. Induced pluripotent stem cells (iPSCs) can generate myogenic progenitors, but their use in combination with bioengineering strategies to modulate their phenotype has not been sufficiently investigated. This review highlights the potential of this combination aimed at pushing the boundaries of skeletal muscle tissue engineering. First, the overall organization and the key steps in the myogenic process occurring in vivo are described. Second, transgenic and non-transgenic approaches for the myogenic induction of human iPSCs are compared. Third, technologies to provide cells with biophysical stimuli, biomaterial cues, and biofabrication strategies are discussed in terms of recreating a biomimetic environment and thus helping to engineer a myogenic phenotype. The embryonic development process and the pro-myogenic role of the muscle-resident cell populations in co-cultures are also described, highlighting the possible clinical applications of iPSCs in the skeletal muscle tissue engineering field.
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Affiliation(s)
- Federica Iberite
- The BioRobotics Institute, Scuola Superiore Sant'Anna, 56127, Pisa (PI), Italy. .,Department of Excellence in Robotics & AI, Scuola Superiore Sant'Anna, 56127, Pisa (PI), Italy.
| | - Emanuele Gruppioni
- Centro Protesi INAIL, Istituto Nazionale per l'Assicurazione contro gli Infortuni sul Lavoro, 40054, Vigorso di Budrio (BO), Italy
| | - Leonardo Ricotti
- The BioRobotics Institute, Scuola Superiore Sant'Anna, 56127, Pisa (PI), Italy.,Department of Excellence in Robotics & AI, Scuola Superiore Sant'Anna, 56127, Pisa (PI), Italy
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18
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Post JN, Loerakker S, Merks R, Carlier A. Implementing computational modeling in tissue engineering: where disciplines meet. Tissue Eng Part A 2022; 28:542-554. [PMID: 35345902 DOI: 10.1089/ten.tea.2021.0215] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In recent years, the mathematical and computational sciences have developed novel methodologies and insights that can aid in designing advanced bioreactors, microfluidic set-ups or organ-on-chip devices, in optimizing culture conditions, or predicting long-term behavior of engineered tissues in vivo. In this review, we introduce the concept of computational models and how they can be integrated in an interdisciplinary workflow for Tissue Engineering and Regenerative Medicine (TERM). We specifically aim this review of general concepts and examples at experimental scientists with little or no computational modeling experience. We also describe the contribution of computational models in understanding TERM processes and in advancing the TERM field by providing novel insights.
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Affiliation(s)
- Janine Nicole Post
- University of Twente, 3230, Tissue Regeneration, Enschede, Overijssel, Netherlands;
| | - Sandra Loerakker
- Eindhoven University of Technology, 3169, Department of Biomedical Engineering, Eindhoven, Noord-Brabant, Netherlands.,Eindhoven University of Technology, 3169, Institute for Complex Molecular Systems, Eindhoven, Noord-Brabant, Netherlands;
| | - Roeland Merks
- Leiden University, 4496, Institute for Biology Leiden and Mathematical Institute, Leiden, Zuid-Holland, Netherlands;
| | - Aurélie Carlier
- Maastricht University, 5211, MERLN Institute for Technology-Inspired Regenerative Medicine, Universiteitssingel 40, 6229 ER Maastricht, Maastricht, Netherlands, 6200 MD;
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19
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Khurana S, Schivo S, Plass JRM, Mersinis N, Scholma J, Kerkhofs J, Zhong L, van de Pol J, Langerak R, Geris L, Karperien M, Post JN. An ECHO of Cartilage: In Silico Prediction of Combinatorial Treatments to Switch Between Transient and Permanent Cartilage Phenotypes With Ex Vivo Validation. Front Bioeng Biotechnol 2021; 9:732917. [PMID: 34869253 PMCID: PMC8634894 DOI: 10.3389/fbioe.2021.732917] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
A fundamental question in cartilage biology is: what determines the switch between permanent cartilage found in the articular joints and transient hypertrophic cartilage that functions as a template for bone? This switch is observed both in a subset of OA patients that develop osteophytes, as well as in cell-based tissue engineering strategies for joint repair. A thorough understanding of the mechanisms regulating cell fate provides opportunities for treatment of cartilage disease and tissue engineering strategies. The objective of this study was to understand the mechanisms that regulate the switch between permanent and transient cartilage using a computational model of chondrocytes, ECHO. To investigate large signaling networks that regulate cell fate decisions, we developed the software tool ANIMO, Analysis of Networks with interactive Modeling. In ANIMO, we generated an activity network integrating 7 signal transduction pathways resulting in a network containing over 50 proteins with 200 interactions. We called this model ECHO, for executable chondrocyte. Previously, we showed that ECHO could be used to characterize mechanisms of cell fate decisions. ECHO was first developed based on a Boolean model of growth plate. Here, we show how the growth plate Boolean model was translated to ANIMO and how we adapted the topology and parameters to generate an articular cartilage model. In ANIMO, many combinations of overactivation/knockout were tested that result in a switch between permanent cartilage (SOX9+) and transient, hypertrophic cartilage (RUNX2+). We used model checking to prioritize combination treatments for wet-lab validation. Three combinatorial treatments were chosen and tested on metatarsals from 1-day old rat pups that were treated for 6 days. We found that a combination of IGF1 with inhibition of ERK1/2 had a positive effect on cartilage formation and growth, whereas activation of DLX5 combined with inhibition of PKA had a negative effect on cartilage formation and growth and resulted in increased cartilage hypertrophy. We show that our model describes cartilage formation, and that model checking can aid in choosing and prioritizing combinatorial treatments that interfere with normal cartilage development. Here we show that combinatorial treatments induce changes in the zonal distribution of cartilage, indication possible switches in cell fate. This indicates that simulations in ECHO aid in describing pathologies in which switches between cell fates are observed, such as OA.
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Affiliation(s)
- Sakshi Khurana
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
| | - Stefano Schivo
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands.,Department of Formal Methods and Tools, CTIT Institute, University of Twente, Enschede, Netherlands
| | - Jacqueline R M Plass
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
| | - Nikolas Mersinis
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
| | - Jetse Scholma
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
| | - Johan Kerkhofs
- Biomechanics Research Unit, GIGA In Silico Medicine, ULiège, Liège, Belgium
| | - Leilei Zhong
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
| | - Jaco van de Pol
- Department of Formal Methods and Tools, CTIT Institute, University of Twente, Enschede, Netherlands.,Dept. of Computer Science, Aarhus University, Aarhus, Denmark
| | - Rom Langerak
- Department of Formal Methods and Tools, CTIT Institute, University of Twente, Enschede, Netherlands
| | - Liesbet Geris
- Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Marcel Karperien
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
| | - Janine N Post
- Technical Medicine Centre, Department of Developmental BioEngineering, University of Twente, Enschede, Netherlands
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20
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Klabukov ID, Krasilnikova OA, Baranovskii DS. Quantitative human physiology: An introduction guide for advanced tissue engineering. Biotechnol J 2021; 17:e2100481. [PMID: 34605205 DOI: 10.1002/biot.202100481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/30/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Ilya D Klabukov
- Department of regenerative technologies and biofabrication, National Medical Research Radiological Center, Obninsk, 249035, Russia
| | - Olga A Krasilnikova
- Laboratory of biomaterials and tissue scaffolds, A. Tsyb Medical Radiological Research Center - Branch of the National Medical Research Radiological Center, Obninsk, 249035, Russia
| | - Denis S Baranovskii
- Department of regenerative technologies and biofabrication, National Medical Research Radiological Center, Obninsk, 249035, Russia
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21
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Coy R, Berg M, Phillips JB, Shipley RJ. Modelling-informed cell-seeded nerve repair construct designs for treating peripheral nerve injuries. PLoS Comput Biol 2021; 17:e1009142. [PMID: 34237052 PMCID: PMC8266098 DOI: 10.1371/journal.pcbi.1009142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/02/2021] [Indexed: 11/19/2022] Open
Abstract
Millions of people worldwide are affected by peripheral nerve injuries (PNI), involving billions of dollars in healthcare costs. Common outcomes for patients include paralysis and loss of sensation, often leading to lifelong pain and disability. Engineered Neural Tissue (EngNT) is being developed as an alternative to the current treatments for large-gap PNIs that show underwhelming functional recovery in many cases. EngNT repair constructs are composed of a stabilised hydrogel cylinder, surrounded by a sheath of material, to mimic the properties of nerve tissue. The technology also enables the spatial seeding of therapeutic cells in the hydrogel to promote nerve regeneration. The identification of mechanisms leading to maximal nerve regeneration and to functional recovery is a central challenge in the design of EngNT repair constructs. Using in vivo experiments in isolation is costly and time-consuming, offering a limited insight on the mechanisms underlying the performance of a given repair construct. To bridge this gap, we derive a cell-solute model and apply it to the case of EngNT repair constructs seeded with therapeutic cells which produce vascular endothelial growth factor (VEGF) under low oxygen conditions to promote vascularisation in the construct. The model comprises a set of coupled non-linear diffusion-reaction equations describing the evolving cell population along with its interactions with oxygen and VEGF fields during the first 24h after transplant into the nerve injury site. This model allows us to evaluate a wide range of repair construct designs (e.g. cell-seeding strategy, sheath material, culture conditions), the idea being that designs performing well over a short timescale could be shortlisted for in vivo trials. In particular, our results suggest that seeding cells beyond a certain density threshold is detrimental regardless of the situation considered, opening new avenues for future nerve tissue engineering.
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Affiliation(s)
- Rachel Coy
- Department of Mechanical Engineering, UCL, London, United Kingdom
- Center for Nerve Engineering, UCL, London, United Kingdom
| | - Maxime Berg
- Department of Mechanical Engineering, UCL, London, United Kingdom
- Center for Nerve Engineering, UCL, London, United Kingdom
- * E-mail:
| | - James B. Phillips
- Center for Nerve Engineering, UCL, London, United Kingdom
- Department of Pharmacology, School of Pharmacy, UCL, London, United Kingdom
| | - Rebecca J. Shipley
- Department of Mechanical Engineering, UCL, London, United Kingdom
- Center for Nerve Engineering, UCL, London, United Kingdom
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